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- PDB-4bge: Crystal structure of InhA(S94A) mutant in complex with pyridomycin -

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Basic information

Entry
Database: PDB / ID: 4bge
TitleCrystal structure of InhA(S94A) mutant in complex with pyridomycin
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD+ binding / peptidoglycan-based cell wall / fatty acid binding / response to antibiotic / plasma membrane
Similarity search - Function
: / Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Pyridomycin / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsPojer, F. / Hartkoorn, R.C. / Cole, S.T.
CitationJournal: Nat. Chem. Biol. / Year: 2014
Title: Pyridomycin bridges the NADH- and substrate-binding pockets of the enoyl reductase InhA.
Authors: Hartkoorn, R.C. / Pojer, F. / Read, J.A. / Gingell, H. / Neres, J. / Horlacher, O.P. / Altmann, K.H. / Cole, S.T.
History
DepositionMar 26, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Nov 21, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_src_gen / entity_src_nat / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity.pdbx_description / _entity.pdbx_mutation / _entity.src_method / _entity_name_com.name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.4Oct 16, 2019Group: Data collection / Other / Category: pdbx_database_status / reflns / reflns_shell
Item: _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs ..._pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rrim_I_all / _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rrim_I_all
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,47612
Polymers171,2336
Non-polymers3,2436
Water13,097727
1
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

D: Enoyl-[acyl-carrier-protein] reductase [NADH]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,3178
Polymers114,1554
Non-polymers2,1624
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation3_545x+1/2,y-1/2,z1
identity operation1_555x,y,z1
Buried area17850 Å2
ΔGint-116.1 kcal/mol
Surface area35420 Å2
MethodPISA
2
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,3178
Polymers114,1554
Non-polymers2,1624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area18360 Å2
ΔGint-118.9 kcal/mol
Surface area35550 Å2
MethodPISA
3
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

D: Enoyl-[acyl-carrier-protein] reductase [NADH]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,3178
Polymers114,1554
Non-polymers2,1624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
MethodPQS
Unit cell
Length a, b, c (Å)100.601, 83.049, 190.682
Angle α, β, γ (deg.)90.00, 94.84, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-ACP reductase / FAS-II enoyl-ACP reductase / NADH-dependent 2-trans-enoyl-ACP reductase


Mass: 28538.781 Da / Num. of mol.: 6 / Mutation: S94A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: inhA, Rv1484, MTCY277.05 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WGR1, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-PYW / Pyridomycin


Mass: 540.565 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H32N4O8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 727 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.93 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorDate: Dec 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 140935 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 31.05 Å2 / Rrim(I) all: 0.141 / Net I/σ(I): 8.5
Reflection shellResolution: 2.25→2.38 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.6 / Rrim(I) all: 0.592 / % possible all: 91.7

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DTI

4dti


Resolution: 2.25→47.5 Å / Cor.coef. Fo:Fc: 0.8173 / Cor.coef. Fo:Fc free: 0.7606 / SU R Cruickshank DPI: 0.395 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.399 / SU Rfree Blow DPI: 0.256 / SU Rfree Cruickshank DPI: 0.258
RfactorNum. reflection% reflectionSelection details
Rfree0.2778 3722 5.03 %RANDOM
Rwork0.2398 ---
obs0.2417 73988 99.42 %-
Displacement parametersBiso mean: 33.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.6731 Å20 Å20.0878 Å2
2---0.3113 Å20 Å2
3---0.9844 Å2
Refine analyzeLuzzati coordinate error obs: 0.487 Å
Refinement stepCycle: LAST / Resolution: 2.25→47.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11651 0 234 727 12612
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00812122HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0516472HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4134SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes267HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1896HARMONIC5
X-RAY DIFFRACTIONt_it12122HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.28
X-RAY DIFFRACTIONt_other_torsion21.84
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1617SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14004SEMIHARMONIC4
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4479 255 4.86 %
Rwork0.3743 4997 -
all0.3777 5252 -
obs--99.42 %

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